Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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	Gene summary
	Malignant transformation analysis
	Malignant transformation related pathway analysis
	Cell-cell communication analysis
	Single-cell gene regulatory network inference analysis
	Somatic mutation of malignant transformation related genes
	Related drugs of malignant transformation related genes

Gene: COL4A3

Gene summary for COL4A3

Gene summary.

Gene information	Species	Human
	Gene symbol	COL4A3
	Gene ID	1285
	Gene name	collagen type IV alpha 3 chain
	Gene Alias	ATS2
	Cytomap	2q36.3
	Gene Type	protein-coding
	GO ID	GO:0001525
	UniProtAcc	Q01955

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Malignant transformation analysis

Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells

Malignant transformation involving gene list.

Entrez ID	Symbol	Replicates	Species	Organ	Tissue	Adj P-value	Log2FC	Malignancy
1285	COL4A3	P15T-E	Human	Esophagus	ESCC	5.20e-29	5.74e-01	0.1149
1285	COL4A3	P24T-E	Human	Esophagus	ESCC	4.12e-11	2.64e-01	0.1287
1285	COL4A3	P26T-E	Human	Esophagus	ESCC	2.55e-31	4.94e-01	0.1276
1285	COL4A3	P28T-E	Human	Esophagus	ESCC	6.56e-15	2.64e-01	0.1149
1285	COL4A3	P31T-E	Human	Esophagus	ESCC	1.30e-15	2.83e-01	0.1251
1285	COL4A3	P32T-E	Human	Esophagus	ESCC	2.13e-27	4.55e-01	0.1666
1285	COL4A3	P37T-E	Human	Esophagus	ESCC	3.20e-21	3.65e-01	0.1371
1285	COL4A3	P38T-E	Human	Esophagus	ESCC	8.07e-09	2.63e-01	0.127
1285	COL4A3	P42T-E	Human	Esophagus	ESCC	1.02e-24	4.84e-01	0.1175
1285	COL4A3	P49T-E	Human	Esophagus	ESCC	1.97e-16	8.99e-01	0.1768
1285	COL4A3	P74T-E	Human	Esophagus	ESCC	7.09e-38	7.35e-01	0.1479
1285	COL4A3	P83T-E	Human	Esophagus	ESCC	4.35e-18	4.58e-01	0.1738
1285	COL4A3	P89T-E	Human	Esophagus	ESCC	6.02e-08	4.15e-01	0.1752
1285	COL4A3	P91T-E	Human	Esophagus	ESCC	1.72e-16	1.05e+00	0.1828
1285	COL4A3	P107T-E	Human	Esophagus	ESCC	4.60e-32	6.88e-01	0.171
1285	COL4A3	P126T-E	Human	Esophagus	ESCC	2.42e-10	6.10e-01	0.1125
1285	COL4A3	TD9	Human	Lung	IAC	2.95e-02	4.40e-01	0.088
1285	COL4A3	RNA-P10T2-P10T2-2	Human	Lung	AAH	7.20e-04	7.53e-01	-0.1406
1285	COL4A3	RNA-P10T2-P10T2-3	Human	Lung	AAH	4.22e-04	7.70e-01	-0.1408
1285	COL4A3	RNA-P10T2-P10T2-4	Human	Lung	AAH	3.20e-03	6.82e-01	-0.138

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
Thyroid		ATC: Anaplastic thyroid cancer
		HT: Hashimoto's thyroiditis
		PTC: Papillary thyroid cancer

∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.

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Malignant transformation related pathway analysis

Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer

Figure of enriched GO biological processes.

Tissue	Disease Stage	Enriched GO biological Processes
Colorectum	AD
Colorectum	SER
Colorectum	MSS
Colorectum	MSI-H
Colorectum	FAP

∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).

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Enriched GO biological processes.

GO ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	Count
GO:0045862111	Esophagus	ESCC	positive regulation of proteolysis	256/8552	372/18723	7.88e-20	9.43e-18	256
GO:2000116111	Esophagus	ESCC	regulation of cysteine-type endopeptidase activity	158/8552	235/18723	1.67e-11	5.90e-10	158
GO:0043281111	Esophagus	ESCC	regulation of cysteine-type endopeptidase activity involved in apoptotic process	143/8552	209/18723	2.12e-11	7.31e-10	143
GO:0010952111	Esophagus	ESCC	positive regulation of peptidase activity	133/8552	197/18723	4.31e-10	1.14e-08	133
GO:0052547111	Esophagus	ESCC	regulation of peptidase activity	275/8552	461/18723	7.54e-10	1.88e-08	275
GO:0052548111	Esophagus	ESCC	regulation of endopeptidase activity	253/8552	432/18723	3.68e-08	6.78e-07	253
GO:0010950111	Esophagus	ESCC	positive regulation of endopeptidase activity	116/8552	179/18723	1.77e-07	2.79e-06	116
GO:0043280110	Esophagus	ESCC	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process	84/8552	129/18723	6.38e-06	6.55e-05	84
GO:2001056110	Esophagus	ESCC	positive regulation of cysteine-type endopeptidase activity	94/8552	148/18723	8.87e-06	8.59e-05	94
GO:000691915	Esophagus	ESCC	activation of cysteine-type endopeptidase activity involved in apoptotic process	54/8552	78/18723	2.17e-05	1.87e-04	54
GO:00301984	Esophagus	ESCC	extracellular matrix organization	171/8552	301/18723	6.08e-05	4.67e-04	171
GO:00430624	Esophagus	ESCC	extracellular structure organization	171/8552	302/18723	7.73e-05	5.76e-04	171
GO:00452294	Esophagus	ESCC	external encapsulating structure organization	172/8552	304/18723	7.80e-05	5.80e-04	172
GO:0045861111	Esophagus	ESCC	negative regulation of proteolysis	195/8552	351/18723	1.13e-04	7.85e-04	195
GO:005067318	Esophagus	ESCC	epithelial cell proliferation	238/8552	437/18723	1.19e-04	8.20e-04	238
GO:0051346110	Esophagus	ESCC	negative regulation of hydrolase activity	208/8552	379/18723	1.76e-04	1.14e-03	208
GO:005067817	Esophagus	ESCC	regulation of epithelial cell proliferation	206/8552	381/18723	5.51e-04	3.02e-03	206
GO:001046620	Esophagus	ESCC	negative regulation of peptidase activity	140/8552	262/18723	6.73e-03	2.46e-02	140
GO:001095119	Esophagus	ESCC	negative regulation of endopeptidase activity	135/8552	252/18723	6.86e-03	2.51e-02	135
GO:00016559	Esophagus	ESCC	urogenital system development	177/8552	338/18723	7.51e-03	2.69e-02	177

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0516510	Esophagus	ESCC	Human papillomavirus infection	215/4205	331/8465	7.86e-09	7.12e-08	3.65e-08	215
hsa0451020	Esophagus	ESCC	Focal adhesion	127/4205	203/8465	1.25e-04	4.99e-04	2.56e-04	127
hsa049268	Esophagus	ESCC	Relaxin signaling pathway	81/4205	129/8465	1.72e-03	5.09e-03	2.61e-03	81
hsa041517	Esophagus	ESCC	PI3K-Akt signaling pathway	197/4205	354/8465	1.24e-02	2.83e-02	1.45e-02	197
hsa0516515	Esophagus	ESCC	Human papillomavirus infection	215/4205	331/8465	7.86e-09	7.12e-08	3.65e-08	215
hsa04510111	Esophagus	ESCC	Focal adhesion	127/4205	203/8465	1.25e-04	4.99e-04	2.56e-04	127
hsa0492616	Esophagus	ESCC	Relaxin signaling pathway	81/4205	129/8465	1.72e-03	5.09e-03	2.61e-03	81
hsa0415114	Esophagus	ESCC	PI3K-Akt signaling pathway	197/4205	354/8465	1.24e-02	2.83e-02	1.45e-02	197
hsa045108	Lung	IAC	Focal adhesion	59/1053	203/8465	1.31e-10	1.06e-08	7.06e-09	59
hsa051656	Lung	IAC	Human papillomavirus infection	71/1053	331/8465	1.88e-06	7.63e-05	5.06e-05	71
hsa049264	Lung	IAC	Relaxin signaling pathway	29/1053	129/8465	9.70e-04	7.32e-03	4.86e-03	29
hsa051464	Lung	IAC	Amoebiasis	23/1053	102/8465	2.99e-03	1.53e-02	1.02e-02	23
hsa04512	Lung	IAC	ECM-receptor interaction	20/1053	89/8465	5.65e-03	2.45e-02	1.63e-02	20
hsa041514	Lung	IAC	PI3K-Akt signaling pathway	60/1053	354/8465	7.03e-03	2.86e-02	1.90e-02	60
hsa0451012	Lung	IAC	Focal adhesion	59/1053	203/8465	1.31e-10	1.06e-08	7.06e-09	59
hsa0516511	Lung	IAC	Human papillomavirus infection	71/1053	331/8465	1.88e-06	7.63e-05	5.06e-05	71
hsa0492612	Lung	IAC	Relaxin signaling pathway	29/1053	129/8465	9.70e-04	7.32e-03	4.86e-03	29
hsa0514611	Lung	IAC	Amoebiasis	23/1053	102/8465	2.99e-03	1.53e-02	1.02e-02	23
hsa045121	Lung	IAC	ECM-receptor interaction	20/1053	89/8465	5.65e-03	2.45e-02	1.63e-02	20
hsa0415111	Lung	IAC	PI3K-Akt signaling pathway	60/1053	354/8465	7.03e-03	2.86e-02	1.90e-02	60

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Cell-cell communication analysis

Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states

Ligand	Receptor	LRpair	Pathway	Tissue	Disease Stage
COL4A3	ITGA1_ITGB1	COL4A3_ITGA1_ITGB1	COLLAGEN	HNSCC	Precancer
COL4A3	ITGA2_ITGB1	COL4A3_ITGA2_ITGB1	COLLAGEN	HNSCC	Precancer
COL4A3	ITGA3_ITGB1	COL4A3_ITGA3_ITGB1	COLLAGEN	HNSCC	Precancer
COL4A3	ITGA9_ITGB1	COL4A3_ITGA9_ITGB1	COLLAGEN	HNSCC	Precancer
COL4A3	ITGAV_ITGB8	COL4A3_ITGAV_ITGB8	COLLAGEN	HNSCC	Precancer
COL4A3	SDC1	COL4A3_SDC1	COLLAGEN	HNSCC	Precancer
COL4A3	SDC4	COL4A3_SDC4	COLLAGEN	HNSCC	Precancer
COL4A3	ITGA1_ITGB1	COL4A3_ITGA1_ITGB1	COLLAGEN	Liver	Precancer
COL4A3	ITGA2_ITGB1	COL4A3_ITGA2_ITGB1	COLLAGEN	Liver	Precancer
COL4A3	ITGA9_ITGB1	COL4A3_ITGA9_ITGB1	COLLAGEN	Liver	Precancer
COL4A3	ITGA10_ITGB1	COL4A3_ITGA10_ITGB1	COLLAGEN	Liver	Precancer
COL4A3	ITGAV_ITGB8	COL4A3_ITGAV_ITGB8	COLLAGEN	Liver	Precancer
COL4A3	CD44	COL4A3_CD44	COLLAGEN	Liver	Precancer
COL4A3	SDC1	COL4A3_SDC1	COLLAGEN	Liver	Precancer
COL4A3	SDC4	COL4A3_SDC4	COLLAGEN	Liver	Precancer
COL4A3	ITGA1_ITGB1	COL4A3_ITGA1_ITGB1	COLLAGEN	Lung	AAH
COL4A3	ITGA2_ITGB1	COL4A3_ITGA2_ITGB1	COLLAGEN	Lung	AAH
COL4A3	ITGA3_ITGB1	COL4A3_ITGA3_ITGB1	COLLAGEN	Lung	AAH
COL4A3	ITGA9_ITGB1	COL4A3_ITGA9_ITGB1	COLLAGEN	Lung	AAH
COL4A3	CD44	COL4A3_CD44	COLLAGEN	Lung	AAH

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Single-cell gene regulatory network inference analysis

Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states

Cell Type

Tissue

Disease Stage

Target Gene

RSS

Regulon Activity

∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.

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Somatic mutation of malignant transformation related genes

Annotation of somatic variants for genes involved in malignant transformation

Hugo Symbol

Variant Class

Variant Classification

dbSNP RS

HGVSc

HGVSp

HGVSp Short

SWISSPROT

BIOTYPE

SIFT

PolyPhen

Tumor Sample Barcode

Tissue

Histology

Sex

Age

Stage

Therapy Types

Drugs

Outcome

COL4A3

SNV

Missense_Mutation

c.1865G>T

p.Gly622Val

p.G622V

Q01955

protein_coding

deleterious(0)

probably_damaging(0.988)

TCGA-3C-AALI-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Poly E

Complete Response

COL4A3

SNV

Missense_Mutation

novel

c.3466G>A

p.Asp1156Asn

p.D1156N

Q01955

protein_coding

tolerated(1)

benign(0.003)

TCGA-5L-AAT1-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

letrozol

COL4A3

SNV

Missense_Mutation

c.2528T>A

p.Ile843Asn

p.I843N

Q01955

protein_coding

tolerated(0.14)

probably_damaging(0.977)

TCGA-A1-A0SO-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

COL4A3

SNV

Missense_Mutation

c.475C>G

p.Pro159Ala

p.P159A

Q01955

protein_coding

tolerated(0.13)

probably_damaging(0.998)

TCGA-A7-A26G-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

COL4A3

SNV

Missense_Mutation

c.964N>A

p.Leu322Ile

p.L322I

Q01955

protein_coding

tolerated(0.12)

possibly_damaging(0.67)

TCGA-A8-A09Q-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

anastrozole

COL4A3

SNV

Missense_Mutation

rs773914532

c.1330N>T

p.Arg444Cys

p.R444C

Q01955

protein_coding

tolerated(0.11)

probably_damaging(0.987)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A3

SNV

Missense_Mutation

novel

c.3679N>T

p.Pro1227Ser

p.P1227S

Q01955

protein_coding

tolerated(0.09)

possibly_damaging(0.557)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A3

SNV

Missense_Mutation

c.835N>G

p.Pro279Ala

p.P279A

Q01955

protein_coding

tolerated(0.15)

probably_damaging(0.994)

TCGA-AN-A0AK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A3

SNV

Missense_Mutation

rs148686474

c.1310N>T

p.Pro437Leu

p.P437L

Q01955

protein_coding

tolerated(0.61)

probably_damaging(0.979)

TCGA-AN-A0AK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

COL4A3

SNV

Missense_Mutation

c.3965N>T

p.Gly1322Val

p.G1322V

Q01955

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AN-A0FN-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

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Related drugs of malignant transformation related genes

Identification of chemicals and drugs interact with genes involved in malignant transfromation

(DGIdb 4.0)

Entrez ID	Symbol	Category	Interaction Types	Drug Claim Name	Drug Name	PMIDs
1285	COL4A3	KINASE, DRUGGABLE GENOME		CHEMBL2108709	COLLAGENASE CLOSTRIDIUM HISTOLYTICUM
1285	COL4A3	KINASE, DRUGGABLE GENOME		CHEMBL2095222	OCRIPLASMIN

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